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Muscle Logic: New Knowledge Resource for Anatomy Enables Comprehensive Searches of the Literature on the Feeding Muscles of Mammals.

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Date
2016
Authors
Druzinsky, Robert E
Balhoff, James P
Crompton, Alfred W
Done, James
German, Rebecca Z
Haendel, Melissa A
Herrel, Anthony
Herring, Susan W
Lapp, Hilmar
Mabee, Paula M
Muller, Hans-Michael
Mungall, Christopher J
Sternberg, Paul W
Van Auken, Kimberly
Vinyard, Christopher J
Williams, Susan H
Wall, Christine E
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(17 total)
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Abstract
BACKGROUND: In recent years large bibliographic databases have made much of the published literature of biology available for searches. However, the capabilities of the search engines integrated into these databases for text-based bibliographic searches are limited. To enable searches that deliver the results expected by comparative anatomists, an underlying logical structure known as an ontology is required. DEVELOPMENT AND TESTING OF THE ONTOLOGY: Here we present the Mammalian Feeding Muscle Ontology (MFMO), a multi-species ontology focused on anatomical structures that participate in feeding and other oral/pharyngeal behaviors. A unique feature of the MFMO is that a simple, computable, definition of each muscle, which includes its attachments and innervation, is true across mammals. This construction mirrors the logical foundation of comparative anatomy and permits searches using language familiar to biologists. Further, it provides a template for muscles that will be useful in extending any anatomy ontology. The MFMO is developed to support the Feeding Experiments End-User Database Project (FEED, https://feedexp.org/), a publicly-available, online repository for physiological data collected from in vivo studies of feeding (e.g., mastication, biting, swallowing) in mammals. Currently the MFMO is integrated into FEED and also into two literature-specific implementations of Textpresso, a text-mining system that facilitates powerful searches of a corpus of scientific publications. We evaluate the MFMO by asking questions that test the ability of the ontology to return appropriate answers (competency questions). We compare the results of queries of the MFMO to results from similar searches in PubMed and Google Scholar. RESULTS AND SIGNIFICANCE: Our tests demonstrate that the MFMO is competent to answer queries formed in the common language of comparative anatomy, but PubMed and Google Scholar are not. Overall, our results show that by incorporating anatomical ontologies into searches, an expanded and anatomically comprehensive set of results can be obtained. The broader scientific and publishing communities should consider taking up the challenge of semantically enabled search capabilities.
Type
Journal article
Subject
Animals
Databases as Topic
Humans
Oropharynx
Pharyngeal Muscles
Search Engine
Permalink
https://hdl.handle.net/10161/11696
Published Version (Please cite this version)
10.1371/journal.pone.0149102
Publication Info
Druzinsky, Robert E; Balhoff, James P; Crompton, Alfred W; Done, James; German, Rebecca Z; Haendel, Melissa A; ... Wall, Christine E (2016). Muscle Logic: New Knowledge Resource for Anatomy Enables Comprehensive Searches of the Literature on the Feeding Muscles of Mammals. PLoS One, 11(2). pp. e0149102. 10.1371/journal.pone.0149102. Retrieved from https://hdl.handle.net/10161/11696.
This is constructed from limited available data and may be imprecise. To cite this article, please review & use the official citation provided by the journal.
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Scholars@Duke

Lapp

Hilmar Lapp

Dir, IT
Wall

Christine Elizabeth Wall

Research Professor Emerita of Evolutionary Anthropology
The focus of my work is the functional and evolutionary anatomy of the head, with an emphasis on how the feeding apparatus works and how it influences and is influenced by other structures and functions. My research focuses primarily on the functional anatomy of extant and extinct primates, but I am also interested in other mammalian groups. Current research projects include: (1) a detailed study of the architecture, fiber types, and the recruitment patterns of the jaw adductor muscl
Alphabetical list of authors with Scholars@Duke profiles.
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